layer23-volume

Reconstructions and analyses from the IARPA MICrONS consortium mouse cortex Layer 2/3 serial EM volume.

Attribution: https://www.microns-explorer.org/terms-and-conditions
Citation: https://www.microns-explorer.org/citation-policy

Over a century ago, Golgi and Cajal revolutionized the field of neuroscience

For an intriguing summary of this revolution, read Mitch Glickstein’s essay on Golgi and Cajal in Current Biology.

Serial LM reconstruction of Golgi stained neuron

Pyramidal neuron of the mouse cortex stained using the Golgi method

Image credit: I created this serial LM reconstruction of a Golgi-stained mouse pyramidal neuron using a Zeiss Photomicroscope II at 40x oil and Smart Objects in Photoshop.

Once again neuroscience is undergoing another revolution with the serial electron microscope brain reconstructions

Petabytes of data have been generated for small volumes (1 cubic mm or less) of human, mouse, songbird, and fly brain volumes. This gargantuan task has been spearheaded by investigators from a variety of entities, including Allen Institute, Baylor, Columbia, Google Research, Harvard, IARPA, Janelia/HHMI, Johns Hopkins, Max Planck Institute, Princeton, Rice, and the University of Cambridge, among others.

Serial EM reconstruction using Neuroglancer

Pyramdial neuron from the Layer 2/3 serial EM volume

Image credit, I created this reconstruction using Neuroglancer of pyramidal neuron with cellid 648518346349538440 in the Layer 2/3 volume.

This github repo focuses on visualization and analyses of the Layer 2/3 EM volume data generated in the IARPA Microns consortium (Allen Institute, Baylor, Princeton). The volume can be viewed in Neuroglancer (developed at Google Research). Allen Institute and the Seung lab at Princeton have posted datasets, resources, analysis tools, and more on their respective github repos, and also at the Allen Brain Map website.

Look up and visualization tools

Use lookup_cellid_in_layer23_volume_neuroglancer.ipynb to identify the cell subtype for a given cellid in the Layer 2/3 volume. This is a human-curated list for cells that contain all (or most) of the cell soma within the volume. Includes a Neuroglancer link generator. See also a version that adds the Neuroglancer nucleus id (for cells with a nucleus in the volume): lookup_cellid_in_layer23_volume_neuroglancer_with_nucleus_id.ipynb.

Use list_of_cell_subtypes_in_layer23_volume.ipynb to view the cellids categorized by cell subtype, from a curated list of 619 cellids.

Use lookup_mitochondria_ids.ipynb to look up mitochondria ids by cellid. Useful for creating a list of mito ids for visualization in neuroglancer and for analyzing voxel data.

Use neuroglancer_link_generator_mitochondria_visualization_version.ipynb to generate a Neuroglancer link for a single cellid and single mitochondrion from the pni_mito_cellswskel_v185_fullstats.csv datatable.

Use neuroglancer_link_generator_all_mitochondria.ipynb to generate a Neuroglancer link for all the mitochondria in a single cellid of interest pulling the mito ids from the 211019_mitochondria_info.csv datatable.

Use vtk_mitochondria_visualizer.ipynb to generate a 3D interactive view of all mitochondria in a cell of interest. Note this method has significant file download and space requirements compared to using the Neuroglancer viewer. Use vtk_mitochondria_visualizer_with_synapses.ipynb to add the pre- and post-synaptic sites to the visualization as well.

Use lookup_synapse_ids.ipynb to look up synapse ids by pre- and post-synaptic cell ids. Also contains voxel data.

Use synapse_visualizer.ipynb to create a 2D and 3D visualization of all pre- and post-synaptic sites on a cell of interest.

Use vtk_nuclei_visualizer_with_vasculature.ipynb to create an interactive 3D visualize the cell nuclei in the volume using vtk and OpenGL. Includes a visualization option to include all vasculature in the volume.

Interesting features in the Layer 2/3 volume

Axon-carrying dendrite

axon_carrying_dendrite folder: a partial neuron (soma is not in the volume) with a possible axon-carrying dendrite.

axon-carrying dendrite

Autapses

autapses folder: there are three autapses in the Layer 2/3 volume and many (24) cases of segmenation errors that are not true autapses.

inhibitory basket neuron autapse

Mitocondria visualizations

mitochondria folder: analysis of interesting mitochondrial features in the layer 2/3 volume, including the largest contiguous mitochondrion in an astrocyte, and the largest number of mitochondria by count in an inhibitory basket neuron.

large contiguous mitochondria in an astrocyte

astrocyte mitochondria folder: analytical and visualization notebooks and high resolution 3D renderings of astrocyte mitochondria.

3D rendering of astrocyte mitochondria colored with a voxel size threshold

Mitochondria analysis and classification

mitochondria analytics folder: more in-depth analysis of the structural, spatial, and positional characteristics of mitochondria in the Layer 2/3 volume.

3D interactive visualization of all mitochondria and synapses in a neuron

Two neurons with the most synapses in the Layer 2/3 volume

most_synapses folder: reconstructions and synaptic analyses of an excitatory pyramidal neuron with the most synapses in the volume, along with an inhibitory basket neuron making the most synapses onto other processes within the volume.

neuron with the most synpases in the layer 2/3 volume

Reciprocal pairs

Pairs of neurons in the Layer 2/3 volume that synapse onto one another

reciprocal_pairs folder: Martinotti-bipolar reciprocal pair (cell ids 648518346349538179 and 648518346349515986, respectively).

Martinotti-bipolar reciprocal pair

An exceptional oligodendrocyte

oligodendrocyte_648518346349508279 folder: a beautiful example of an oligocyte in the layer 2/3 volume. Images of myelination as well as an example of mis-segmentation where a synaptic bouton from a nearby axon was incorrectly segmented to the oligodendrocyte cell.

oligodendrocyte myelinating a neuronal process

3D nuclei visualizer with vasculature

vtk_nuclei_visualizer_with_vasculature.ipynb: notebook to create a 3D visualization of cell nuclei in the Layer 2/3 volume. Uses meshparty, vtk, and OpenGL. Here, nuclei from excitatory neurons is shown in light blue; nuceli from inhibitory neurons in light red, and nuclei from glial cells are shown in olive green. Vasculature in the Layer 2/3 volume is shown in light grey.

3D interactive visualization with nuclei colored by cell type and including vasculature

Thank you for stopping by!

Drop me an email if you have any questions or would like to collaborate. Shawn